GgaINT0078828 @ galGal3
Intron Retention
Gene
ENSGALG00000009360 | CAPN2
Description
NA
Coordinates
chr3:18807008-18807761:-
Coord C1 exon
chr3:18807601-18807761
Coord A exon
chr3:18807178-18807600
Coord C2 exon
chr3:18807008-18807177
Length
423 bp
Sequences
Splice sites
5' ss Seq
CAAGTAAGA
5' ss Score
7.61
3' ss Seq
TTCGTAAATCTGCTTCACAGACA
3' ss Score
5.62
Exon sequences
Seq C1 exon
GATGGCCTTCAATGACTTCCTGAGGCACTACTCCCGCCTGGAAATCTGCAATCTGACTCCAGACACTCTGGCAAGTGACAGGTACAAGAAGTGGAGCCTGCTGAAGCTGGATGGGAACTGGCGGCGAGGAGCTACTGCGGGGGGCTGCAGGAATTACCCAA
Seq A exon
GTAAGAGTGTGCTCATCCGCTTGTTGCTCTGGGAGCTTCAGTGTCCAGGTAGATATTCTGCAGTGTAAAGGATTGGGTTGAAGCCATAGCCCCAGTGGCACAGTGGTGAGGAACCTTTCTGAGAGTGATGTAATATTGACTTTGGTGCTGGCTTTGGTCAGCCCTGCATGCCTAACACACCCTTGTCCTTGATGTTCACTGGTCTGGGGTGACTTATGACGTGCTGGAAGCATCAGGGACTGATATCCAGGAAGTGCAAGTGCATGGAAGACACGGCTCCATAATGAGGGTCTACTTGTGGTTGTGAGGCTGGAAGGGAAGCATTGGTCACAGCTTAATTTGGAAGTCACGGCTGTATCTATCCTAGCTGGCATGTGTTTATCAAAGATAGTTCTGAGCAGTTTTCGTAAATCTGCTTCACAG
Seq C2 exon
ACACTTTCTGGACGAATCCACAGTATTTAATCAAGCTGGAGGAAGAAGATGAGGATCCTGATGATCCTGAGGGGGGCTGCACATTTCTCATTGGCCTGATTCAGAAGCATCGGAGGAAGCAGAGGAAGATGGGAGAGGACATGCATACCATTGGCTTTGCAATTTATGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000009360:ENSGALT00000015241:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.087
Domain overlap (PFAM):
C1:
PF0064816=Peptidase_C2=PD(6.3=34.5),PF0106717=Calpain_III=PU(15.4=43.6)
A:
NA
C2:
PF0106717=Calpain_III=FE(35.9=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GATGGCCTTCAATGACTTCCTGA
R:
AAATTGCAAAGCCAATGGTATGCA
Band lengths:
326-749
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]